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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cellxgenedp.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings cellxgenedp_1.7.2.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/cellxgenedp.Rcheck'
* using R Under development (unstable) (2024-03-16 r86144 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'cellxgenedp/DESCRIPTION' ... OK
* this is package 'cellxgenedp' version '1.7.2'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'cellxgenedp' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
query  15.55   2.22   17.78
facets  6.90   0.78    7.69
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
    1. ├─base::vapply(datasets[column_names], class, character(1)) at test-datasets.R:34:5
    2. ├─datasets[column_names]
    3. ├─tibble:::`[.tbl_df`(datasets, column_names)
    4. │ └─tibble:::vectbl_as_col_location(...)
    5. │   ├─tibble:::subclass_col_index_errors(...)
    6. │   │ └─base::withCallingHandlers(...)
    7. │   └─vctrs::vec_as_location(j, n, names, missing = "error", call = call)
    8. └─vctrs (local) `<fn>`()
    9.   └─vctrs:::stop_subscript_oob(...)
   10.     └─vctrs:::stop_subscript(...)
   11.       └─rlang::abort(...)
  
  [ FAIL 2 | WARN 0 | SKIP 3 | PASS 46 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  'F:/biocbuild/bbs-3.19-bioc/meat/cellxgenedp.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL cellxgenedp
###
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* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'cellxgenedp' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cellxgenedp)

R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(cellxgenedp)
Loading required package: dplyr

Attaching package: 'dplyr'

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

The interface to CELLxGENE has changed; versions of cellxgenedp prior
to 1.4.1 / 1.5.2 will cease to work when CELLxGENE removes the previous
interface. See the section 'API changes' of the 'Discover and download
datasets...' vignette for important details.
> 
> test_check("cellxgenedp")
[ FAIL 2 | WARN 0 | SKIP 3 | PASS 46 ]

══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On CRAN (2): 'test-cellxgene.R:8:5', 'test-cellxgene.R:35:5'
• files_download() not tested due to mockery limitation (1):
  'test-files.R:21:5'

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-datasets.R:33:5'): datasets() works ──────────────────────────
all(column_names %in% names(datasets)) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
── Error ('test-datasets.R:34:5'): datasets() works ────────────────────────────
<vctrs_error_subscript_oob/vctrs_error_subscript/rlang_error/error/condition>
Error in `datasets[column_names]`: Can't subset columns that don't exist.
x Column `batch_condition` doesn't exist.
Backtrace:
     ▆
  1. ├─base::vapply(datasets[column_names], class, character(1)) at test-datasets.R:34:5
  2. ├─datasets[column_names]
  3. ├─tibble:::`[.tbl_df`(datasets, column_names)
  4. │ └─tibble:::vectbl_as_col_location(...)
  5. │   ├─tibble:::subclass_col_index_errors(...)
  6. │   │ └─base::withCallingHandlers(...)
  7. │   └─vctrs::vec_as_location(j, n, names, missing = "error", call = call)
  8. └─vctrs (local) `<fn>`()
  9.   └─vctrs:::stop_subscript_oob(...)
 10.     └─vctrs:::stop_subscript(...)
 11.       └─rlang::abort(...)

[ FAIL 2 | WARN 0 | SKIP 3 | PASS 46 ]
Error: Test failures
Execution halted